FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
Ps2Ex3M1_Heter_6month_07_07_2016_F3_80_Fem_R1.fastq.gz 35,207,030 0 150-150 47
Ps2Ex3M1_Heter_6month_07_07_2016_F3_80_Fem_R2.fastq.gz 35,207,030 0 150-150 47
Ps2Ex3M1_Heter_6month_07_07_2016_F3_81_Fem_R1.fastq.gz 35,203,765 0 150-150 47
Ps2Ex3M1_Heter_6month_07_07_2016_F3_81_Fem_R2.fastq.gz 35,203,765 0 150-150 47
Ps2Ex3M1_Heter_6month_07_07_2016_F3_84_Fem_R1.fastq.gz 34,329,340 0 150-150 52
Ps2Ex3M1_Heter_6month_07_07_2016_F3_84_Fem_R2.fastq.gz 34,329,340 0 150-150 52
Ps2Ex3M1_Heter_6month_07_07_2016_F3_89_Fem_R1.fastq.gz 37,144,975 0 150-150 46
Ps2Ex3M1_Heter_6month_07_07_2016_F3_89_Fem_R2.fastq.gz 37,144,975 0 150-150 47
Ps2Ex3M1_Hom_6month_07_07_2016_F3_78_Fem_R1.fastq.gz 35,271,163 0 150-150 47
Ps2Ex3M1_Hom_6month_07_07_2016_F3_78_Fem_R2.fastq.gz 35,271,163 0 150-150 46
Ps2Ex3M1_Hom_6month_07_07_2016_F3_82_Fem_R1.fastq.gz 31,423,430 0 150-150 47
Ps2Ex3M1_Hom_6month_07_07_2016_F3_82_Fem_R2.fastq.gz 31,423,430 0 150-150 46
Ps2Ex3M1_Hom_6month_07_07_2016_F3_83_Fem_R1.fastq.gz 33,701,029 0 150-150 47
Ps2Ex3M1_Hom_6month_07_07_2016_F3_83_Fem_R2.fastq.gz 33,701,029 0 150-150 47
Ps2Ex3M1_Hom_6month_07_07_2016_F3_85_Fem_R1.fastq.gz 34,855,462 0 150-150 47
Ps2Ex3M1_Hom_6month_07_07_2016_F3_85_Fem_R2.fastq.gz 34,855,462 0 150-150 47
Ps2Ex3M1_WT_6month_07_07_2016_F3_79_Fem_R1.fastq.gz 27,979,654 0 150-150 47
Ps2Ex3M1_WT_6month_07_07_2016_F3_79_Fem_R2.fastq.gz 27,979,654 0 150-150 47
Ps2Ex3M1_WT_6month_07_07_2016_F3_86_Fem_R1.fastq.gz 32,642,121 0 150-150 47
Ps2Ex3M1_WT_6month_07_07_2016_F3_86_Fem_R2.fastq.gz 32,642,121 0 150-150 46
Ps2Ex3M1_WT_6month_07_07_2016_F3_88_Fem_R1.fastq.gz 34,587,957 0 150-150 48
Ps2Ex3M1_WT_6month_07_07_2016_F3_88_Fem_R2.fastq.gz 34,587,957 0 150-150 48
Ps2Ex3M1_WT_6month_07_07_2016_F3_95_Fem_R1.fastq.gz 32,013,598 0 150-150 46
Ps2Ex3M1_WT_6month_07_07_2016_F3_95_Fem_R2.fastq.gz 32,013,598 0 150-150 46

Read Totals

Library Sizes ranged between 27,979,654 and 37,144,975 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Drerio Transcriptome

GC Content Distributions for all reads showing theoretical GC content from the Drerio Transcriptome

Sequence Length Distribution

Sequence Duplication Levels

Adapter Content

Universal Adapter Content

Overrepresented Summary

Total overrepresented sequences for each library

Overrepresented Sequences

Summary of the most overrepresented sequences in all files. A maximum of 30 sequences are shown
Sequence Total Present In Overall Percentage Max_Percentage Possible_Source
GGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCATC 3,339,092 12 0.41288653% 1.0877472% No Hit
GTGGGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGC 3,315,886 12 0.41001705% 1.7212301% No Hit
CTCCTGAAAAGGTTGTATCCTTTGTTAAAGGGGCTGTACCCTCTTTAACT 3,115,607 11 0.38525209% 1.1064811% No Hit
CGAGAGGCTCTAGTTGATATACTACGGCGTAAAGGGTGGTTAAGGAACAA 2,868,527 12 0.35470007% 1.0066840% No Hit
CTGGGGGAGCGGCCGCCCCGCGGCGCCCCCTCTCGTTCCCGTCTCCGGAG 2,624,978 10 0.32458466% 1.6869389% No Hit
GTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCATCT 2,393,631 12 0.29597807% 0.7904521% No Hit
CCGCTGTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATCC 2,260,750 12 0.27954702% 1.3219363% No Hit
CCTCCTTCAAGTATTGTTTCATGTTACATTTTCGTATATTCTGGGGTAGA 2,190,300 12 0.27083571% 0.8235987% No Hit
GGGCCTCTAGCATCTAAAAGCGTATAACAGTTAAAGGGCCGTTTGGCTTT 1,834,366 11 0.22682364% 0.6824629% No Hit
GGCCCGGCGCACGTCCAGAGTCGCCGCCGCACACCGCAGCGCATCCCCCC 1,833,990 9 0.22677715% 1.3068238% No Hit
GGCCCGGCGCACGTCCAGAGTCGCCGCCGCGCACCGCAGCGCATCCCCCC 1,726,933 10 0.21353930% 1.0327696% No Hit
CCCGCTGTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATC 1,415,136 12 0.17498487% 0.7909444% No Hit
CTGGGAGATGAATAAAAGTTCAGCTTCGTACACCCCAAATTAAAAAATTA 1,331,991 10 0.16470380% 0.4751368% No Hit
GGCCTCTAGCATCTAAAAGCGTATAACAGTTAAAGGGCCGTTTGGCTTTA 1,327,074 10 0.16409580% 0.5252067% No Hit
GGGGGAGCGGCCGCCCCGCGGCGCCCCCTCTCGTTCCCGTCTCCGGAGCG 1,283,696 9 0.15873201% 0.8684758% No Hit
GGGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCAT 1,238,093 12 0.15309309% 0.7816557% No Hit
GGGGTGTACGAAGCTGAACTTTTATTCATCTCCCAGACAACCAGCTATTG 1,195,276 12 0.14779867% 1.0729480% No Hit
GCCCACTACGACAACGTGTTTTGTAAATTATGATCTTTATTCTCCTGAAA 1,153,870 10 0.14267872% 0.4318004% No Hit
CAGTGGCGTGCGCCTGTAATCCAAGCTACTGGGAGGCTGAGGCTGGCGGA 1,108,764 11 0.13710126% 0.6433564% No Hit
CGGGTCGGGTGGGTGGCCGGCATCACCGCGGACCTCGGGCGCCCTTTTGG 1,081,549 12 0.13373606% 0.7325573% No Hit
GCCTATTTAACTTAGGGCCAACCCGTCTCTGTGGCAATAGAGTGGGAAGA 976,789 12 0.12078224% 0.4683734% No Hit
CTCCTTCAAGTATTGTTTCATGTTACATTTTCGTATATTCTGGGGTAGAA 966,254 10 0.11947956% 0.3931156% No Hit
CTTAGACGACCTGGTAGTCCAAGGCTCCCCCAGGAGCACCATATCGATAC 949,672 11 0.11742916% 0.5371236% No Hit
GAAGAAATTCATAATTCTGACAATAATATCTTACTTCCCTAAAAATACCA 937,910 10 0.11597476% 0.3691791% No Hit
ATAAAAGTTCAGCTTCGTACACCCCAAATTAAAAAATTAAATTTAATTTA 926,299 9 0.11453904% 0.4176627% No Hit
GGGGTAACGATGTCTGTTGTGGATTTTTCTCAGTTTTTAACTCACATTGC 909,247 10 0.11243052% 0.3494484% No Hit
AGCTGGGGAGATCCGCGAGAAGGGCCCGGCGCACGTCCAGAGTCGCCGCC 886,590 11 0.10962893% 0.5268700% No Hit
CTCTAGTTGATATACTACGGCGTAAAGGGTGGTTAAGGAACAATGTAAAA 877,203 12 0.10846820% 0.4243199% No Hit
GGTCGGGTGGGTGGCCGGCATCACCGCGGACCTCGGGCGCCCTTTTGGAC 865,450 11 0.10701491% 0.4498572% No Hit
GGGTGGGTGGCCGGCATCACCGCGGACCTCGGGCGCCCTTTTGGACGTGG 815,363 10 0.10082154% 0.4953081% No Hit

Session Information

R version 3.6.1 (2019-07-05)

Platform: x86_64-pc-linux-gnu (64-bit)

locale: LC_CTYPE=en_AU.UTF-8, LC_NUMERIC=C, LC_TIME=en_AU.UTF-8, LC_COLLATE=en_AU.UTF-8, LC_MONETARY=en_AU.UTF-8, LC_MESSAGES=en_AU.UTF-8, LC_PAPER=en_AU.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_AU.UTF-8 and LC_IDENTIFICATION=C

attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: readr(v.1.3.1), stringr(v.1.4.0), magrittr(v.1.5), scales(v.1.1.0), pander(v.0.6.3), kableExtra(v.1.1.0), dplyr(v.0.8.3), ngsReports(v.1.1.4), tibble(v.2.1.3), ggplot2(v.3.2.1) and BiocGenerics(v.0.32.0)

loaded via a namespace (and not attached): bitops(v.1.0-6), matrixStats(v.0.55.0), lubridate(v.1.7.4), webshot(v.0.5.1), RColorBrewer(v.1.1-2), httr(v.1.4.1), GenomeInfoDb(v.1.22.0), tools(v.3.6.1), backports(v.1.1.5), R6(v.2.4.1), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.1.2), tidyselect(v.0.2.5), compiler(v.3.6.1), rvest(v.0.3.5), Biobase(v.2.46.0), Cairo(v.1.5-10), flashClust(v.1.01-2), xml2(v.1.2.2), DelayedArray(v.0.12.0), plotly(v.4.9.1), ggdendro(v.0.1-20), labeling(v.0.3), digest(v.0.6.22), Rsamtools(v.2.2.1), rmarkdown(v.1.17), XVector(v.0.26.0), pkgconfig(v.2.0.3), htmltools(v.0.4.0), fastmap(v.1.0.1), FactoMineR(v.1.42), highr(v.0.8), htmlwidgets(v.1.5.1), rlang(v.0.4.1), rstudioapi(v.0.10), shiny(v.1.4.0), farver(v.2.0.1), zoo(v.1.8-6), hwriter(v.1.3.2), jsonlite(v.1.6), crosstalk(v.1.0.0), BiocParallel(v.1.20.0), RCurl(v.1.95-4.12), GenomeInfoDbData(v.1.2.2), leaps(v.3.0), Matrix(v.1.2-17), Rcpp(v.1.0.3), munsell(v.0.5.0), S4Vectors(v.0.24.0), lifecycle(v.0.1.0), scatterplot3d(v.0.3-41), stringi(v.1.4.3), yaml(v.2.2.0), MASS(v.7.3-51.4), SummarizedExperiment(v.1.16.0), zlibbioc(v.1.32.0), plyr(v.1.8.4), grid(v.3.6.1), promises(v.1.1.0), crayon(v.1.3.4), lattice(v.0.20-38), Biostrings(v.2.54.0), hms(v.0.5.2), zeallot(v.0.1.0), knitr(v.1.26), pillar(v.1.4.2), GenomicRanges(v.1.38.0), reshape2(v.1.4.3), stats4(v.3.6.1), glue(v.1.3.1), evaluate(v.0.14), ShortRead(v.1.44.0), latticeExtra(v.0.6-28), data.table(v.1.12.6), httpuv(v.1.5.2), vctrs(v.0.2.0), gtable(v.0.3.0), purrr(v.0.3.3), tidyr(v.1.0.0), assertthat(v.0.2.1), xfun(v.0.11), mime(v.0.7), xtable(v.1.8-4), later(v.1.0.0), viridisLite(v.0.3.0), truncnorm(v.1.0-8), GenomicAlignments(v.1.22.1), IRanges(v.2.20.0), cluster(v.2.1.0) and ellipsis(v.0.3.0)